[English] 日本語
Yorodumi
- EMDB-21845: The V1 region of human V-ATPase in state 1 (focused refinement) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21845
TitleThe V1 region of human V-ATPase in state 1 (focused refinement)
Map dataThe V1 region of human V-ATPase in state 1 (focused refinement)
Sample
  • Complex: Human V-ATPase and SidK complex
    • Complex: Human V-ATPase
      • Protein or peptide: V-type proton ATPase catalytic subunit A
      • Protein or peptide: V-type proton ATPase subunit B, brain isoform
      • Protein or peptide: V-type proton ATPase subunit E 1
      • Protein or peptide: V-type proton ATPase subunit G 1
      • Protein or peptide: V-type proton ATPase subunit D
      • Protein or peptide: V-type proton ATPase subunit F
    • Complex: SidK
      • Protein or peptide: SidK
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsV-ATPase / proton pump / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / ATPase-coupled ion transmembrane transporter activity / cellular response to increased oxygen levels / Golgi lumen acidification / Transferrin endocytosis and recycling / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane ...proton-transporting two-sector ATPase complex / Ion channel transport / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / intracellular pH reduction / ATPase-coupled ion transmembrane transporter activity / cellular response to increased oxygen levels / Golgi lumen acidification / Transferrin endocytosis and recycling / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / lysosomal lumen acidification / endosomal lumen acidification / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase complex / ROS and RNS production in phagocytes / protein localization to cilium / vacuolar acidification / proton-transporting V-type ATPase complex / proton transmembrane transporter activity / microvillus / cilium assembly / regulation of macroautophagy / specific granule membrane / ATP metabolic process / H+-transporting two-sector ATPase / ruffle / Insulin receptor recycling / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / secretory granule / cilium / synaptic vesicle membrane / melanosome / ATPase binding / intracellular iron ion homeostasis / endosome / endosome membrane / apical plasma membrane / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
ATPase, V1 complex, subunit A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V1 complex, subunit D / V-type ATPase subunit E / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / V-type ATPase subunit E, C-terminal domain superfamily ...ATPase, V1 complex, subunit A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V1 complex, subunit D / V-type ATPase subunit E / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / ATP synthase (E/31 kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase subunit G 1 / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase subunit E 1 / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit F / Type IV secretion protein Dot / V-type proton ATPase subunit D
Similarity search - Component
Biological speciesHomo sapiens (human) / Legionella pneumophila subsp. pneumophila (bacteria) / Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang L / Wu H
CitationJournal: Mol Cell / Year: 2020
Title: Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly.
Authors: Longfei Wang / Di Wu / Carol V Robinson / Hao Wu / Tian-Min Fu /
Abstract: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton ...Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the V complex. We define ATP6AP1 as a structural hub for V complex assembly because it connects to multiple V subunits and phospholipids in the c-ring. The glycolipids and the glycosylated V subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids.
History
DepositionApr 20, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wlz
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21845.png

Downloads & links

-
Map

FileDownload / File: emd_21845.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe V1 region of human V-ATPase in state 1 (focused refinement)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å		1.08 Å/pix.
x 360 pix.
= 388.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-2.5068724 - 4.18343
Average (Standard dev.)0.0039131674 (±0.094889075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z388.800388.800388.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-2.5074.1830.004

-
Supplemental data

-
Sample components

+
Entire : Human V-ATPase and SidK complex

EntireName: Human V-ATPase and SidK complex
Components
  • Complex: Human V-ATPase and SidK complex
    • Complex: Human V-ATPase
      • Protein or peptide: V-type proton ATPase catalytic subunit A
      • Protein or peptide: V-type proton ATPase subunit B, brain isoform
      • Protein or peptide: V-type proton ATPase subunit E 1
      • Protein or peptide: V-type proton ATPase subunit G 1
      • Protein or peptide: V-type proton ATPase subunit D
      • Protein or peptide: V-type proton ATPase subunit F
    • Complex: SidK
      • Protein or peptide: SidK
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: Human V-ATPase and SidK complex

SupramoleculeName: Human V-ATPase and SidK complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

+
Supramolecule #2: Human V-ATPase

SupramoleculeName: Human V-ATPase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4-#7
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: SidK

SupramoleculeName: SidK / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)

+
Macromolecule #1: V-type proton ATPase catalytic subunit A

MacromoleculeName: V-type proton ATPase catalytic subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.379875 KDa
SequenceString: MDFSKLPKIL DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWDFTPCK NLRVGSHITG GDIYGIVSEN S LIKHKIML ...String:
MDFSKLPKIL DEDKESTFGY VHGVSGPVVT ACDMAGAAMY ELVRVGHSEL VGEIIRLEGD MATIQVYEET SGVSVGDPVL RTGKPLSVE LGPGIMGAIF DGIQRPLSDI SSQTQSIYIP RGVNVSALSR DIKWDFTPCK NLRVGSHITG GDIYGIVSEN S LIKHKIML PPRNRGTVTY IAPPGNYDTS DVVLELEFEG VKEKFTMVQV WPVRQVRPVT EKLPANHPLL TGQRVLDALF PC VQGGTTA IPGAFGCGKT VISQSLSKYS NSDVIIYVGC GERGNEMSEV LRDFPELTME VDGKVESIMK RTALVANTSN MPV AAREAS IYTGITLSEY FRDMGYHVSM MADSTSRWAE ALREISGRLA EMPADSGYPA YLGARLASFY ERAGRVKCLG NPER EGSVS IVGAVSPPGG DFSDPVTSAT LGIVQVFWGL DKKLAQRKHF PSVNWLISYS KYMRALDEYY DKHFTEFVPL RTKAK EILQ EEEDLAEIVQ LVGKASLAET DKITLEVAKL IKDDFLQQNG YTPYDRFCPF YKTVGMLSNM IAFYDMARRA VETTAQ SDN KITWSIIREH MGDILYKLSS MKFKDPLKDG EAKIKSDYAQ LLEDMQNAFR SLED

UniProtKB: V-type proton ATPase catalytic subunit A

+
Macromolecule #2: V-type proton ATPase subunit B, brain isoform

MacromoleculeName: V-type proton ATPase subunit B, brain isoform / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.5615 KDa
SequenceString: MALRAMRGIV NGAAPELPVP TGGPAVGARE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE ...String:
MALRAMRGIV NGAAPELPVP TGGPAVGARE QALAVSRNYL SQPRLTYKTV SGVNGPLVIL DHVKFPRYAE IVHLTLPDGT KRSGQVLEV SGSKAVVQVF EGTSGIDAKK TSCEFTGDIL RTPVSEDMLG RVFNGSGKPI DRGPVVLAED FLDIMGQPIN P QCRIYPEE MIQTGISAID GMNSIARGQK IPIFSAAGLP HNEIAAQICR QAGLVKKSKD VVDYSEENFA IVFAAMGVNM ET ARFFKSD FEENGSMDNV CLFLNLANDP TIERIITPRL ALTTAEFLAY QCEKHVLVIL TDMSSYAEAL REVSAAREEV PGR RGFPGY MYTDLATIYE RAGRVEGRNG SITQIPILTM PNDDITHPIP DLTGYITEGQ IYVDRQLHNR QIYPPINVLP SLSR LMKSA IGEGMTRKDH ADVSNQLYAC YAIGKDVQAM KAVVGEEALT SDDLLYLEFL QKFERNFIAQ GPYENRTVFE TLDIG WQLL RIFPKEMLKR IPQSTLSEFY PRDSAKH

UniProtKB: V-type proton ATPase subunit B, brain isoform

+
Macromolecule #3: SidK

MacromoleculeName: SidK / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513
Molecular weightTheoretical: 65.505297 KDa
SequenceString: MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILQ ELLRLVSSIS PFKMKLDLIE SQYEKMKQHV NLWKSDYHVK LNQLNQLTDY LKNAAPTPKN NFLRAMTSVL Q MQIAQYGI ...String:
MSFIKVGIKM GGLTSEQYHS QVVGKIGYIA RCMQTIDPEN NLKKIREDYQ DVLIWAEKNY RFEEILEASK SGKCPNDLDA LSRRSLILQ ELLRLVSSIS PFKMKLDLIE SQYEKMKQHV NLWKSDYHVK LNQLNQLTDY LKNAAPTPKN NFLRAMTSVL Q MQIAQYGI TEDNEGINQL FKLGLHLLAM ANEKIDEQYH LFKGYVKDQP EESPFEGILP AEDQKILVKT MIDYAMPKLS SK VLQDKLS ALSSSDVLTK TLLDSIDRIV KENEKLNALS KVKLGKFGLD IREIEVIYSQ ALKISPQDAL QYTAQQCDAQ LLS MAFPDS QNYIIESISN KKVKTIAELI HSKEFIYQII KTEVFKQVDP NEKIRLQAAT ELYQLLGRIM DKQINLFTKM NLEQ INEYI QTKTKAILDK IPERVELLTF MGFEIPTFKG IETLMTDISH SQDNETLAIA QEFYTNIKNA KNQLLGDKLI EDITP QDVE KFFNQCSQYG SEAAEKLADN RPVLTKIADI LTAIARWAIS LIGFNTPPQF LAPTRTCVDQ VSDEITKIKL KLEDTL GSL QKVQEESLSL

UniProtKB: Type IV secretion protein Dot

+
Macromolecule #4: V-type proton ATPase subunit E 1

MacromoleculeName: V-type proton ATPase subunit E 1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.183346 KDa
SequenceString: MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K NDVDVQID ...String:
MALSDADVQK QIKHMMAFIE QEANEKAEEI DAKAEEEFNI EKGRLVQTQR LKIMEYYEKK EKQIEQQKKI QMSNLMNQAR LKVLRARDD LITDLLNEAK QRLSKVVKDT TRYQVLLDGL VLQGLYQLLE PRMIVRCRKQ DFPLVKAAVQ KAIPMYKIAT K NDVDVQID QESYLPEDIA GGVEIYNGDR KIKVSNTLES RLDLIAQQMM PEVRGALFGA NANRKFLD

UniProtKB: V-type proton ATPase subunit E 1

+
Macromolecule #5: V-type proton ATPase subunit G 1

MacromoleculeName: V-type proton ATPase subunit G 1 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.781547 KDa
SequenceString:
MASQSQGIQQ LLQAEKRAAE KVSEARKRKN RRLKQAKEEA QAEIEQYRLQ REKEFKAKEA AALGSRGSCS TEVEKETQEK MTILQTYFR QNRDEVLDNL LAFVCDIRPE IHENYRING

UniProtKB: V-type proton ATPase subunit G 1

+
Macromolecule #6: V-type proton ATPase subunit D

MacromoleculeName: V-type proton ATPase subunit D / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.311918 KDa
SequenceString: MSGKDRIEIF PSRMAQTIMK ARLKGAQTGR NLLKKKSDAL TLRFRQILKK IIETKMLMGE VMREAAFSLA EAKFTAGDFS TTVIQNVNK AQVKIRAKKD NVAGVTLPVF EHYHEGTDSY ELTGLARGGE QLAKLKRNYA KAVELLVELA SLQTSFVTLD E AIKITNRR ...String:
MSGKDRIEIF PSRMAQTIMK ARLKGAQTGR NLLKKKSDAL TLRFRQILKK IIETKMLMGE VMREAAFSLA EAKFTAGDFS TTVIQNVNK AQVKIRAKKD NVAGVTLPVF EHYHEGTDSY ELTGLARGGE QLAKLKRNYA KAVELLVELA SLQTSFVTLD E AIKITNRR VNAIEHVIIP RIERTLAYII TELDEREREE FYRLKKIQEK KKILKEKSEK DLEQRRAAGE VLEPANLLAE EK DEDLLFE

UniProtKB: V-type proton ATPase subunit D

+
Macromolecule #7: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.38821 KDa
SequenceString:
MAGRGKLIAV IGDEDTVTGF LLGGIGELNK NRHPNFLVVE KDTTINEIED TFRQFLNRDD IGIILINQYI AEMVRHALDA HQQSIPAVL EIPSKEHPYD AAKDSILRRA RGMFTAEDLR

UniProtKB: V-type proton ATPase subunit F

+
Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1000000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more